RRNA promoters

Figure 12.16 DNA and RNA recognition by the fifth zinc finger of TMIIA. (a) The zinc finger recognizes bases in the major groove of 5S rRNA promoter DNA. (b) The finger recognizes the phosphate groups of 5S rRNA. (From Tanaka Hall, 2005. Copyright 2005, with permission from Elsevier.)...

The 100- to 160-kb chloroplast genomes (Chapter 23, Section E,2) also have many prokaryotic features. They encode 50 proteins as well as the tRNAs and rRNAs. Promoter and terminator sequences resemble those of bacteria and protein sequences are often homologous to those in bacteria. This applies, for example, to the a, (3, and (3 subunits of RNA polymerase.685... 

The rRNA promoter consists of a core element which straddles the transcriptional start site (designated as position +1) from residues -31 to +6 plus an upstream control element (UCE) about 50-80 bp in size and located about 100 bp upstream from the start site (i.e. at position -100 Fig. 4b). A transcription factor called upstream binding factor (UBF) binds both to the UCE as well as to a region next to and overlapping with the core element. Interestingly, TATA box binding protein (TBP see Topic G6), also binds to the rRNA promoter (in fact, TBP is required for initiation by all three eukaryotic RNA polymerases). The UBF and TBP transcription factors interact with each other and with RNA Pol I to form a transcription initiation complex. The RNA Pol I then transcribes... 

Analysis of the sequences located upstream of archaeal rRNA genes has shown that archaeal rRNA promoters consist of the sequence TTTA(A/T)A located 20-30 nucleotides upstream of the transcription initiation site and a weakly conserved sequence, (A/T)TG(A/C) around the transcription initiation site [40]. Transcription of the rRNA genes terminates within pyrimidine-rich regions in the extreme thermophiles [30,41], in pyrimidine-rich regions followed by a short hairpin loop in the methanogens [27,34] and in AT-rich regions preceded by a GC-rich region in the extreme... 

FIGURE 12.20 (a) TFIIIA binds to 5S rRNA promoter sequences using zinc fingers 1—3, 5, and 7—9 which recognise respectively box C... 

Three general transcription factors are required for Pol III to Initiate transcription of tRNA and SS-rRNA genes In vitro. Two multimeric factors, TFIIIC and TFIIIB, participate In Initiation at both tRNA and SS-rRNA promoters a third factor, TFIIIA, Is required for initiation at SS-rRNA promoters. As with assembly of Pol I and Pol II Initiation complexes, the Pol III general transcription factors bind to promoter DNA in a defined sequence. 

An essential factor required for accurate RNA Pol I transcription is the selectivity factor SL1 (SL1 Clos et al., 1986a Learned et al., 1985). As mentioned earlier, SL1 is also a species-specific factor that directs promoter-specific transcription in the presence of its cognate template. SL1 does not bind specifically to the rRNA promoter however, in the presence of UBF, it forms a strong cooperative DNA-binding complex at the ribosomal DNA promoter that is critical for initiation of transcription (Bell et al., 1988, 1989 Learned et al., 1986). Mutations in the promoter sequences that affect either the binding of UBF to the DNA template or the interaction of UBF with SL1 result in drastic reduction of transcription activity (Bell et al., 1988). These findings indicate that the interactions between UBF and its DNA recognition sequence, and between UBF and SL1, play a major role in RNA Pol I transcription. For many years the molecular identification of SL1 has proven a difficult task. The... 

FIGURE 26-5 Typical E. coli promoters recognized by an RNA polymerase holoenzyme containing a70. Sequences of the nontemplate strand are shown, read in the 5 —>3 direction, as is the convention for representations of this kind. The sequences vary from one promoter to the next, but comparisons of many promoters reveal similarities, particularly in the —10 and -35 regions. The sequence element UP, not present in all E. coli promoters, is shown in the P1 promoter for the highly expressed rRNA gene rrnB. UP elements, generally occur-... 

RNA polymerase I (Pol I) is responsible for the synthesis of only one type of RNA, a transcript called pre-ribosomal RNA (or pre-rRNA), which contains the precursor for the 18S, 5.8S, and 28S rRNAs (see Fig. 26-22). Pol I promoters vary greatly in sequence from one species to another. The principal function of RNA polymerase II (Pol II) is synthesis of mRNAs and some specialized RNAs. This enzyme can recognize thousands of promoters that vary greatly in sequence. Many Pol II promoters have a few sequence features in common, including a TATA box (eukaryotic consensus sequence TATAAA) near base pair —30 and an Inr sequence (initiator) near the RNA start site at +1 (Fig. 26-8). 

A typical rRNA (rrn) operon contains two promoters and genes for 16S, 23S, and 5S rRNA and a single 4S tRNA gene. The four fully processed RNAs are derived from a single intact 30S primary transcript. 

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